SWISS-MODEL Repository - Model Details

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1
1147

Sequence
UniProt Q9U489
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q9U489: 6239.C12C8.3a

Domain
Link to: [ InterPro ]
Filamin
NHL
NHL
NHL
NHL
NHL
NHL

Model 3D Structure
Model information:
Modelled residue range: 691 to 820
Based on template: [ 4umg ]  
Sequence Identity [%]: 78%
Model date: 2015-05-07
Revision date: 2015-05-05

Quaternary structure information: [details]
Template (4umg): MONOMER
Model: MONOMER

Ligand information: [details]
Ligands in the template: none.
Ligands in the model: none.
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

Alignment

TARGET    1       SGPCAKNS SIVGDSFKKA IRERQTVIYV QLRDACGDLL SSSIAATQPT
4umg_1#6  691     sgpcakns sivgdsfkka irerqtviyv qlrdacgdll s---------
                                                                      
TARGET                     sss    sss ss   sssss ssss   sss  hhh      
4umg_1#6                   sss    sss ss   sssss ssss   sss           


TARGET    49    SQALLPHQEP HSHLEQAMPT SDVQAFVISP DGSTVEVTMT PRENGIVALS
4umg_1#6  758   ---------- ---------t sdvqafvisp dgstvevtmt prengivals
                                                                      
TARGET                      hhhhhhh    ssssssss    sss  sss ss  ssssss
4umg_1#6                               ssssssss    sss  sss ss  ssssss


TARGET    99    YYPSIEGSYT LNILVKGTPI SGCPTTMDIR RG                   
4umg_1#6  789   yypsiegsyt lnilvkgtpi sgcpttmdir rg-                  
                                                                      
TARGET          s     ssss ssssss sss     ssssss                      
4umg_1#6        s     ssss ssssss sss     ssssss                      



Quality


Template's ligands section
Template without ligands.
No ligands were included in the model.


Quaternary Structure Annotation of the Template
4umg is annotated as MONOMER
The oligomeric state of the structure was assigned by the authors of the corresponding PDB entry
The following biological unit was used to build the template structure: 4umg.pdb1.gz

Quaternary Structure Modelling of the Target Protein
The quaternary structure can be assumed to be identical
Model was succesfully built as MONOMER.


Template Selection
 - Start SMR-Pipeline for:3f8ab73484fdb769038270bf2f68a84e on BC2-cluster at Thu May  7 16:22:32
2015 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

 - Warning: sequence length exceeded the limit of 1000 residues
 - HHsearch profile build is skipped
 - Warning: Oligomer Prediction was not successfull!

 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:1): model based on new templates
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                                 *********
 - building model based on 4umgA (691-820) was successful 
 - Repository Pipeline parameter

   Cut-off parameters to model the target based on a BLAST target-template alignment
    Evalue :                                     0.0001
    Minimum Template size (aa) for ranking :     25
    Minimum Sequence identity :                  60

   Cut-off parameters to model the target based on a HHSearch target-template alignment
    Evalue :                                     0.0001
    Probability :                                50
    MAC :                                        0.3

   Parameters for model selection
    Minimal number of uncovered target
     residues after BLAST to run HHSEARCH :      50
    Minimal number of uncovered target
     residues to model an additional template :  25
    
 - Finish SMR-Pipeline for:3f8ab73484fdb769038270bf2f68a84e on BC2-cluster at Thu May  7 16:23:10
2015 




Template Description
Match Chain SeqId

4umg: CRYSTAL STRUCTURE OF THE LIN-41 FILAMIN DOMAIN
Solved by: X-RAY, Resolution: 1.68A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

691-820 4umgA 78%
[Model]

Downloads
Reference

If you are using models from the SWISS-MODEL Repository, please cite the following articles:

- Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009).
The SWISS-MODEL Repository and associated resources.
Nucleic Acids Res. 37, D387-D392.

- Jürgen Kopp and Torsten Schwede (2004)
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.
Nucleic Acids Res. 32, D230-D234.




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